The WCKD soldiers apparently don't know the basics of armed combat. They don't seek cover or concealment when firing their weapons, they have scoped weapons but don't use that to their advantage; and they shoot before they have their targets acquired.
Just before the cure is applied to the little girl at WCKD headquarters. A square reflection of the camera is seen in the eye's of the girl when she is laying on the medical table with the lights above during a close-up of her face.
When Thomas is listening the the speech to the just rescued kids at the shipwreck yard in the beginning of the movie, you can see movie equipment like a TV monitor reflecting in his eyes. Anything but content related.
When at the coastal encampment while looking at the map to the "City", the city circled on the map is where Denver is located. After Thomas and the others are rescued from the tunnel, Jorge remarks that they almost made it a whole day. Then, during that conversation they come to a stop outside the "City" in question. Appearing to have driven from the Pacific coast to Denver in the same day, a drive of over 1,000 miles.
The VTOL aircraft are chasing a 4x4 across broken terrain. Since the 4x4 couldn't possibly go faster than 60-70 MPH on that type of terrain, an aircraft couldn't "chase" them without stalling.. Additionally, it wouldn't need to as it could simply fly ahead of it and shoot it from the front.
When the VTOL goes to the top of the WCKD headquarters they bank right to turn right. That is seen from the cockpit. The horizon instrument stays horizontal compared to the plane but it should move to be aligned with the actual horizon. The cockpit instruments are a still picture.
The goof item below may give away important plot points.
When Ava Paige is shot, she is standing face to face with Thomas. The shot clearly goes in her back, and when she is lying on her back on the ground after, she is clearly bleeding on the front. If the bullet went through her back and front and she is facing Thomas, it should have hit him too.